21-20405418-T-C

Variant names:

• chr21-20405418-T-C
• rs1888414

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.608 in 151,960 control chromosomes in the GnomAD database, including 28,559 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.61 (28559 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.980
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92294 AN: 151842 Hom.: 28547 Cov.: 31

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.612

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.608 AC: 92338 AN: 151960 Hom.: 28559 Cov.: 31 AF XY: 0.611 AC XY: 45364 AN XY: 74284

African (AFR) AF: 0.602 AC: 24958 AN: 41448

American (AMR) AF: 0.480 AC: 7325 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 2382 AN: 3468

East Asian (EAS) AF: 0.769 AC: 3958 AN: 5146

South Asian (SAS) AF: 0.704 AC: 3385 AN: 4810

European-Finnish (FIN) AF: 0.647 AC: 6839 AN: 10572

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.609 AC: 41397 AN: 67944

Other (OTH) AF: 0.615 AC: 1296 AN: 2108

Alfa AF: 0.592 Hom.: 19748

Bravo AF: 0.599

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.24
DANN	Benign	0.48
PhyloP100		-0.98

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1888414; hg19: chr21-21777730;